I'm thinking that it's not wise to test for things like
overall_percentage_identity etc in alignments that are generated by
external software like T-Coffee, Clustalw etc. Changes to software
algorithms/efficiency, bug fixes etc may well alter the quality of the
alignment produced in different versions and thus affect the value
returned by such methods. Therefore, I think these methods should only
be tested from alignments loaded directly from t/data.
Nath